#!/usr/bin/env python
# -*- coding: utf-8 -*-

import sys
import os
import argparse
from ConfigParser import SafeConfigParser
from glob import iglob
import my
import job

#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_1_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 1 --barcodes TTAGGCA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_3_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 3 --barcodes TTAGGCA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_2_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 2 --barcodes TTAGGCA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_5_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 5 --barcodes TTAGGCA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_4_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 4 --barcodes TTAGGCA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_7_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 7 --barcodes GATCAGA GCCAATA ACAGTGA ACTTGAA CAGATCA TTAGGCA CGATGTA CTTGTAA TGACCAA GGCTACA ATCACGA TAGCTTA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test
#--file1s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_1_0068_qseq.txt --file2s /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_3_0068_qseq.txt --qseqtagfiles /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0001_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0002_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0003_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0004_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0005_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0006_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0007_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0008_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0021_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0022_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0023_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0024_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0025_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0026_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0027_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0028_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0041_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0042_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0043_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0044_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0045_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0046_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0047_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0048_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0061_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0062_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0063_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0064_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0065_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0066_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0067_qseq.txt /data/storage-1-02/solexa/110511_SN430_0243_B817FLABXX/Data/Intensities/BaseCalls/s_6_2_0068_qseq.txt --exptrun 110511_SN430_0243_B817FLABXX --lane 6 --barcodes GATCAGA GCCAATA ACAGTGA ACTTGAA CAGATCA TTAGGCA CGATGTA CTTGTAA TGACCAA GGCTACA ATCACGA TAGCTTA --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test

#--file1s /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_1208_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_1_2208_qseq.txt --file2s /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_1208_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_3_2208_qseq.txt --qseqtagfiles /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_1208_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2101_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2102_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2103_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2104_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2105_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2106_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2107_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2108_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2201_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2202_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2203_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2204_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2205_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2206_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2207_qseq.txt /data/storage-1-02/archive/myourshaw/illumina/110623_SN860_0067_2011-100R_A81MVKABXX/Data/Intensities/BaseCalls/QSEQ/s_8_2_2208_qseq.txt --exptrun 110623_SN860_0067_2011-100R_A81MVKABXX --lane 8 --barcodes TTAGGCA ACAGTGA GCCAATA CTTGTAA --default_barcode_file None --novobarcode /share/apps/myourshaw/novocraft-current/novobarcode --readgroup_dir /scratch1/tmp/myourshaw/gmd/qseq2rg-test2

def main():

	#command line arguments
	parser = argparse.ArgumentParser(parents=[my.get_directory_parser()],
		description = '<barcoded qseq files> > readgroup_dir/exptrun.lane.read.barcode_qseq.txt.gz',
		epilog = 'pypeline.qseq2rg_novobarcode_and_cat version 1.0β1 ©2011-2012 Michael Yourshaw all rights reserved')
	parser.add_argument('--file1s', required=True, nargs='+',
											help='list of read1 qseq files belonging to the same illumina experiment run lane')
	parser.add_argument('--file2s', nargs='*',
											help='list of read3 qseq files belonging to the same illumina experiment run lane')
	parser.add_argument('--qseqtagfiles', required=True,  nargs='+',
											help='list of barcode read qseq files belonging to the same illumina experiment run lane')
	parser.add_argument('--exptrun', required=True,
											help='experiment run id')
	parser.add_argument('--lane', required=True,
											help='illumina lane')
	parser.add_argument('--barcodes', required=True, nargs='+',
											help='barcodes')
	parser.add_argument('--default_barcode_file',
											help='string = default novobarcode-style tag list')
	parser.add_argument('--novobarcode',
											help='path to novobarcode executable (required if barcodes are given) (default: from config->novobarcode)')
	parser.add_argument('--readgroup_qseqs_dir', required=True,
											help='output readgroup directory')
	args = parser.parse_args()
	my.set_directory_defaults(args)
	config = my.get_config(args)

	novobarcode = args.novobarcode if args.novobarcode and my.is_exe(args.novobarcode) else config.get('novocraft','novobarcode')

	novobarcode_tmpdir = my.unique_dir('novobarcode_{}_tmp'.format(args.exptrun), args.tmp_dir)

	if my.file_exists(args.default_barcode_file):
		tagfile = args.default_barcode_file
		tagfile_fd = open(tagfile,'r')
	else:
		tagfile_fd, tagfile = my.unique_file(os.path.join(novobarcode_tmpdir,'tagfile_tmp'))
		tagfile_fd.writelines(
"""Distance 3
Format N 5
01 ATCACGA
02 CGATGTA
03 TTAGGCA
04 TGACCAA
05 ACAGTGA
06 GCCAATA
07 CAGATCA
08 ACTTGAA
09 GATCAGA
10 TAGCTTA
11 GGCTACA
12 CTTGTAA
"""
)
		tagfile_fd.close()

	#novobarcode job array
	cmds = []
	novobarcode_output_dir = my.unique_dir('novobarcode_{}_lane_{}'.format(args.exptrun, args.lane), novobarcode_tmpdir)
	for i in range(len(args.file1s)):
		file1 = args.file1s[i]
		file2 = args.file2s[i] if args.file2s else ''
		qseqtagfile = args.qseqtagfiles[i]
		cmds.append('{0} -b {1} -d {2} -F QSEQ -f {3} {4} -i {5} --ILQ_SKIP --QSEQ_OUT --NC_OFF;'\
		 .format(novobarcode, tagfile, novobarcode_output_dir, file1, file2, qseqtagfile))
	jobName = 'novobarcode_{}.{}_{}'.format(args.exptrun, args.lane, my.localtime_squish())
	my.print_log('job {} started; commands:\n{}'.format(jobName, '\n'.join(cmds)))
	j = job.Job(jobName = jobName,
	outputPath = args.qout_dir, errorPath = args.qout_dir, workingDirectory = novobarcode_tmpdir,
	email = args.email, blockEmail = not args.sendemailforintermediatejobs)
	try:
		j.executeCommands(cmds, synchronous=True)
	except Exception as e:
		my.print_err('There was an error running the job {}:\n{}\nintermediate files are in {}'.format(jobName, e, novobarcode_tmpdir))
	else:
		my.print_log('job {} finished; status:\n{}'.format(jobName, '\n'.join(j.completionMsg)))
		with open(os.path.join(novobarcode_tmpdir,'{}_job_status_report.txt'.format(jobName)), 'w') as s:
			s.write(format('\n'.join(j.completionMsg)))

	#cat job array
		cmds = []
		all_barcodes = my.get_immediate_subdirectory_names(novobarcode_output_dir)
		barcodes = all_barcodes if len(args.barcodes) == 1 and (args.barcodes == '*' or my.file_exists(args.barcodes)) else args.barcodes
		for barcode in barcodes:
			qseq_dir = os.path.join(novobarcode_output_dir, barcode)
			for read in ('1','2','3'):
				compressed = False
				qseqs = my.get_qseqs(qseq_dir, args.lane, read, gz=False)
				if not qseqs:
					compressed = True
					qseqs = my.get_qseqs(qseq_dir, args.lane, read, gz=True)
				if compressed:
					cmds.append('gzip -cd {} | cat - | gzip > {}'.format(' '.join(qseqs), os.path.join(args.readgroup_dir,'{}.{}.{}.{}_qseq.txt.gz'.format(args.exptrun, args.lane, read, barcode))))
				else:
					cmds.append('cat {} | gzip > {}'.format(' '.join(qseqs), os.path.join(args.readgroup_dir,'{}.{}.{}.{}_qseq.txt.gz'.format(args.exptrun, args.lane, read, barcode))))
		jobName = 'novobarcode_cat_{}.{}_{}'.format(args.exptrun, args.lane, my.localtime_squish())
		my.print_log('job {} started; commands:\n{}'.format(jobName, '\n'.join(cmds)))
		j = job.Job(jobName = jobName,
		outputPath = args.qout_dir, errorPath = args.qout_dir, workingDirectory = novobarcode_tmpdir,
	email = args.email, blockEmail = not args.sendemailforintermediatejobs)
	try:
		j.executeCommands(cmds, synchronous=True)
	except Exception as e:
		my.print_err('There was an error running the job {}:\n{}\nintermediate files are in {}'.format(jobName, e, novobarcode_tmpdir))
	else:
		my.print_log('job {} finished; status:\n{}'.format(jobName, '\n'.join(j.completionMsg)))
		with open(os.path.join(novobarcode_tmpdir,'{}_job_status_report.txt'.format(jobName)), 'w') as s:
			s.write(format('\n'.join(j.completionMsg)))
		if args.deletetempfiles:
			shutil.rmtree(novobarcode_tmpdir, ignore_errors=True)

if __name__ == "__main__": sys.exit(main())
